Shadow Academy
by XxCherriesandChocolatexX
Summary: AU- Misty, May, Dawn and Leaf are very successful killers. One day they get a mission that orders them to travel and attend Shadow Academy, a school hidden long ago in the mountains. Their mission? To capture and kill four boys for reasons unknown. But what happens when they uncover things that were meant to stay hidden? Can they find the truth about their past? PSCSISLGS
1. Character Profiles

Agent: Waterflower, Misty

Codename: Aqua

Age: 15

Status: Elite level assassin

Current location: Mount Moon Base

Current mission status: Codename O.S.A

Rank: Elite

Training: Assassination, Combat, Weaponry

Skills: Combat and Weapons, known for her 'Misty Mallet'

Group: Sister of – Group Shadow

Area: Infiltration and Field work

Connections: Unknown

Home: Kanto, Unknown

Other: Taken in at birth due to unknown circumstances, found by Cynthia. No known family. Excels in water activities and any water based mission. Has a fiery attitude and those that get on her wrong side feel the wrath of her 'Misty Mallet' due to her temper. Masters in combat and weaponry. Misty is the main fighter of Group Shadow, and will protect her 'sisters' at all costs.

Agent: Green, Leaf

Codename: Flora

Age: 15

Status: Elite level assassin

Current location: Mount Moon Base

Current mission status: Codename O.S.A

Rank: Elite

Training: Assassination, Stealth, Combat

Skills: Hand-to-hand combat and shadowing

Group: Sister of – Group Shadow

Area: Infiltration and Field work

Connections: Unknown

Home: Kanto, Unknown

Other: Taken in at birth due to unknown circumstances, found by Cynthia. No known family as of yet. Excels in shadowing and fighting, and despite her training has a cheerful and child- like persona. Agent Leaf is the Leader of Group Shadow, and due to her experience in stealth is how the group tracker.

Agent: Maple, May

Codename: Thorn

Age: 15

Status: Elite level assassin

Current location: Mount Moon Base

Current mission status: Codename O.S.A

Rank: Elite

Training: Assassination, Poisonous & Medicinal Herbs

Skills: Poison & Remedies

Group: Sister of – Group Shadow

Area: Infiltration and Field work

Connections: Norman Maple, Petalburg Gym Leader, Father

Caroline Maple, Norman Maple's Wife, Mother

Max Maple, Normal and Caroline Maple's son, Brother

Home: Hoenn, Petalburg

Other: Taken in at birth due to unknown circumstances, found by Cynthia. Loves to eat, can be naïve but has a knack for anything to do with plants. Still retains innocent and childlike aspects of her personality but is a very experienced agent. Is knowledgeable of the properties of several types of different remedies and poisons. Acts as the healer of Group Shadow and makes up the poisons they use in missions.

Agent: Berlitz, Dawn

Codename: Pearl

Age: 15

Status: Elite level assassin

Current mission status: Codename O.S.A

Rank: Elite

Training: Assassination, Mechanical Devices, Computerised objects

Skills: Computer hacking, technical whiz

Group: Sister of – Group Shadow

Area: Infiltration and Field work

Connections: Sinnoh, Unknown

Home: Unknown

Other: Taken in at an early age due to unknown circumstances, found by Cynthia. Can hack into anything in very little time, loves fashion and obsessed with the colour pink. She has the role of collecting data on the enemy, gathering information and is how the group access their target most of the time.

Name: Ash Ketchum

Mission name: Raven,

Nickname: Moron/Idiot

Age: 15

Status: High level student at Shadow Academy

Current location: Shadow Academy

Current mission status: N/A

Rank: High

Training: Defence and weaponry

Weapons of choice: Bow & arrow, dagger

Group: Aura

Area: Protection and Defence

Connections: Delia Ketchum, Mother

Home: Kanto, Pallet Town

Other: Born into Shadow Academy. Constantly eats his weight worth in food, and though he can be 'dense', he has a kind heart and will always help those in need. Despite his dense nature, he has a knack for the bow and arrow. He hits targets from a long range distance, but unlike Paul attacks in the open.

Name: Gary Oak

Mission Name: Ace

Nickname: Player

Age: 15

Status: High level student

Current location: Shadow Academy

Current mission status: N/A

Rank: High

Training: Defence and weaponry

Weapon of choice: Katana (Single)

Group: Aura

Area: Protection and Defence

Connections: Professor Samuel Oak, Pokemon Researcher, Grandfather

Home: Kanto, Pallet Town

Other: Born into Shadow Academy. Loves to flirt with girls, constantly seen with either his group members or a female. Not much known about his past, other than the fact that he is the nephew of Samuel Oak. He is the Leader of Group Aura, therefore always goes straight forward into attack; usually tag-teaming with Drew.

Name: Drew Hayden

Mission name: Forest

Nickname/s: Grassy, Moss or The Green Vegetable

Age: 15

Status: High level student at Shadow Academy

Current location: Shadow Academy

Current mission status: N/A

Rank: High

Training: Defence and weaponry

Weapons of choice: Kama (Double)

Group: Aura

Area: Protection and Defence

Connections: Solidad, Shadow Academy's Elite Defence Team, Guardian

Home: Hoenn, Unknown

Other: Born into Shadow Academy. Excellent with double Kama blades, has an 'arrogant' attitude and a strange love for flowers; roses in particular. Usually performs missions by fighting alongside Gary, due to his preferred battle tactic of 'head on attack'.

Name: Paul Shinji

Mission Name: Onyx

Nickname: Shade

Age: 15

Status: High level student at Shadow Academy

Current location: Shadow Academy

Current mission status: N/A

Rank: High

Training: Defence and weaponry

Weapons of choice: Throwing Stars, Throwing Knives, long range distance attacks

Group: Aura

Area: Protection and Defence

Connections: Reggie Shinji, Veilstone City's Gym Leader

Home: Sinnoh, Veilstone

Other: Born into Shadow Academy. Cold personality, usually acts as the groups 'take out' man, due to his knack of long range weapons, and will attack first before Gary goes into battle. He usually reminds hidden during attack but will constantly move around.

For some reason, when I was searching up different weapons I thought that a 'haribo' was a blade because I'd seen it somewhere before. Turns out it's just a Gummy Bear brand *sweatdrops* I wonder if you could Gummy Bear someone to death…..


	2. Prologue

**Bet you weren't expecting this were you? Well I thought since Secrets Of The Past got a Prologue, I should probably make one for this. For those of you that are new here; Welcome to the story!**

_Shadow Academy – Prologue_

The day our lives fell apart was a day none of us would ever forget. It was the day it all began, and the day it all ended. I should have known to never to go against the rules, I should never have let my feelings for _them_ get in the way. None of us should have. We should have known better.

_We lost everything._

We were trained not to let our emotions get in the way, to bury them down deep inside us. Feelings were a liability, nothing but an obstacle that would only get in the way of missions. That's what we were taught to believe, and I never knew just how dangerous they could be.

_We let them get the better of us._

We were trained to kill. They had taught us to be merciless, ruthless and deceiving. Never to trust anyone outside the organisation. We were trained to be heartless. Masters of disguise and deceit, trained in the art of killing. It was all we had ever known, our entire lives had been spent in the dark.

_My sisters and I._

There were four of us; Thorn, Pearl, Aqua and I. All trained to be the ultimate killers; never forgiving, never forgetting. We were the sisters of Group Shadow; the most feared squad of assassins in all the regions. They were my life, the very being of my existence.

_The Sisters of Group Shadow._

We were the best of the best, the number one squad out of the whole organisation. Even better than the boss herself. Only the most important and top secret missions were given to us. We had brought down countless bases, organisations, undercover operations and several of the finest Leaders of every region. Even the most high ranking Elites had never stood a chance.

_We never failed._

Everyone knew our name, though nobody but the boss had ever seen our faces. That was another rule that we always had to obey, not matter the consequence; never reveal your identity.

_Another rule we broke._

The Shadow Sisters name had left its mark on every corner of the world. We were quick and professional, we couldn't afford to slip up. No target we were given ever escaped, none of them ever got the chance.

_Except them._

Until we broke the number one rule of all assassins, the one thing that an assassin should never do. My sisters and I committed the ultimate crime, something they had taught us not to do since the very first day of training.

_We fell in love._

But it was worse than that. We didn't just fall in love with anyone, no. It would have been much simpler, it wouldn't have been so bad if we had fallen for anyone but _them_. Not only had we broken one of the only two rules that could cost us our lives, but we did something far more terrible than that.

_We fell in love with our enemy._

Had I of known that the day we were given that assignment would be the day my world would crumble down I never would have said yes. If I knew back then that it was _them_ who would be our targets we could have turned away. I would have walked out of that office with my sisters, and everything would have been okay. None of this would have happened.

_But we didn't._

I was their Leader; it was my job to keep them safe. But I didn't, I only let it happen, and it shouldn't have. I could have spared my sisters all of the pain, all of the hurt, could have saved them the loss. I could have also spared _them_.

_But I didn't._

My name is Flora, we are the Shadow Sisters, and this is our story…


	3. New Beginnings

**Wow, there were so many positive responses for the Prologue! I definitely wasn't expecting that, so thank you all so much. I LURVE CHU ALL! Also just to let you know, I've changed the Character Profiles a bit. Under the section 'other' it's got different information now, so if you've already read it before this chapter was posted I suggest you re-read it to avoid any confusion.**

**Just giving you a fair warning; if you don't like death or violence, turn away now. It's rated like that for a reason. There won't be any actual anime character deaths exactly, but there will be death. Confused? Good.**

* * *

**Sorry for any grammatical errors, my Beta is currently unavailable. I WAS to wait to post this, but a few people *eyes certain friends* have talked me into it :P**

* * *

**I don't own Pokemon, or anything else in this story except for the code names, and even then I nicked them off of Google…**

_Shadow Academy – The Beginning_

**Johto Headquarters, Silvertown – Normal POV**

Two figures crept silently through the night, carefully manoeuvring their way through an empty hallway. Both were dressed from head to toe in black clothing that consisted of; a top, pants, belt, boots, gloves and mask. One figure, with an elaborate embroided green leaf sewn onto their left glove, held up their hand to signal her companion to stop.

Her bright, green eyes swept over the mechanical door in front of them, analyzing it carefully. The door was completely barricaded, as well as several complicated looking locks that would set off loud shrills if one tried to enter without permission. To the left, a flashing red light caught her eye where a keypad was attached.

Just by looking at the thing, she could tell it would be impossible to break through. They _were_ in one of the most heavily guarded places in all of Johto after all. To most, doing this was unthinkable. It was impossible.

"Flora to Pearl, are you there?" she asked, flipping the switch on her earpiece and whispering softly into the intercom.

Static sounds buzzed through the device before a voice replied, "Pearl here. I'm just getting into the system now, you'll be in faster than Thorn at lunch time."

"Hey! I resent that you know," another voice whined.

The girl known as Flora rolled her eyes. "Thorn, we're on a mission, you can complain about remarks later. How long until we're in Pearl?"

"Almost got it, just one more an-voila! You're in," the voice replied triumphantly.

A beeping sound came from ahead as Pearl finished speaking, and the red light blinked green as an access sound rang from it.

"You're a genius," Flora muttered.

"I try."

"Okay, Pearl you need to get out of there now and get to Thorn. Thorn, you stay on guard and make sure she gets to you safely," she commanded.

"Check," the two replied firmly, switching off their earpieces.

"Are you ready, Aqua?" Flora questioned, turning to her silent companion.

A pair of bright blue eyes stared back with excitement. "Oh Flora, aren't I always?" the figure smiled, holding up their right glove to give an 'OK' sign. In the small amount of light, a flash of blue fashioned into a water droplet could be seen.

"Then let's do this," Flora smiled. Stepping forward, she typed a few buttons on the keypad and smirked in satisfaction as the door opened quietly.

They entered through immediately, moving in alignment down the corridor that would lead right to their targets. After several minutes, the echoes of hushed voices could be heard, and two looked at each other knowingly.

Each took off at the same time, both running swiftly to reach where the sounds were emanating from. They passed many different rooms, none of which were of any use to either girl. Soon enough, the two arrived outside an open doorway with the shadow of two figures visible from the hall.

Flora gave Aqua a sign to stop running, and they swiftly made their way to where their targets were located. Each pulled out their chosen weapons; a small dagger. Weapons such as this weren't normally used for high rank missions, but they needed to get the job done as quick and clean as possible.

In the flash of an eye, the two burst into the room. Their targets; one male and one female, eyes widened in shock, a champagne glass crashing to the floor in the process. Before they could even register what was happening, Flora gave another signal and the male hit the floor with a thud.

The woman barely had time to open her mouth as Flora raised her dagger, and struck.

* * *

**Johto Headquarters, Silvertown – Normal POV**

"Oof!"

"Ow, Dawn!"

"Sorry! Hey, no using real names on missions," the girl reminded her, wagging a finger in her friends face.

"We're only on watch duty, and there's no one around. Now could you get off of me?" Thorn grumbled in response.

Pearl quickly shot up, holding out a hand to her dishevelled teammate. Thorn ignored the offer and picked herself up instead, brushing down her clothes. Pearl rolled her eyes, before reaching up and pulling off her mask, letting her long blue hair cascade down her back.

Thorn's eyes widened at her actions. "What are you doing? Someone might see us!" she whispered frantically.

"Oh would you relax? You said it yourself, there's no one around anyway," the blunette pointed out. Heavy footsteps were heard and the the two of them quickly ducked out of sight as a burly guard walked past, lazily scanning the area before walking off again. "Besides that guy," she added, seeing the unamused expression Thorn was giving her.

"Very comforting," Thorn remarked sarcastically.

"I'm entitled to mistakes," Pearl pouted.

"Some assassin you are," she winked teasingly.

"Oh please, we all know I'm fabulous," Pearl stated in a fake valley-girl accent, striking a pose and flicking her hair.

Thorn laughed at her friends antics, "Well, we _are_ members of Group Shadow after all."

"Speaking of Group Shadow members, where do you think the other two are?" the blunette asked.

The girl just shrugged in response, pulling out a chocolate bar from nowhere.

"Very helpful," Pearl deadpanned.

"I doubt it will take long, they never do," Thorn replied in mid-bite.

"You're right about that," a different voice spoke up, causing them to whip around in shock. Two hands covered their mouths, muffling the scream that the two released.

"Oh would you two chickens calm down? It's just us!" Aqua revealed, uncovering their mouths as they gasped for air.

"Aqua! Don't do that," Pearl pouted, glaring at the girl while Thorn clutched her heart for dear life.

The two newcomers chuckled at their friends reactions, "Sorry Pearly, we couldn't help it," Flora giggled, before her voice turned more serious. "Now, care to explain why you have your face showing to the world?"

The girl squeaked and hurriedly put her mask back on, glancing at Flora sheepishly. "Oops, sorry," she responded in a muffled voice.

Flora just rolled her eyes at the girl before turning to Thorn, "How long do we have?"

"Not long, security passed by a few minutes ago," the girl answered.

"That means we don't have long. They've probably almost reached the door," Aqua spoke up.

_**BEEP! BEEP! BEEP! BEEP!**_

All four snapped their heads up as the now triggered alarm echoed throughout the building, and red flashing lights activated all around them.

"Scratch that, we need to get out of here!"

* * *

**The streets of Silvertown, Johto - Normal POV**

Flashes of green, blue, red and pink sparkled in the moonlight as the four assassins moved in sync across the rooftops, each girl landing with precision and grace that had taken years to perfect. To anyone looking above from the street below they would have looking nothing more than a mere shadow or trick of the light.

Flora, who was the furthest ahead, crouched down and attached her fingers together to make a flat surface and held it away from her body. The girl behind her; Thorn, leapt onto the makeshift landing pad and Flora sprang her high up into the air. Flora then jumped up and grabbed each of Thorn's hands, flipping therself through the air to gain extra height. Using each other's momentum, they landed with exact accuracy onto the next building.

A soft thud was heard behind the two as Pearl and Aqua landed next to them, mimicking their movements perfectly. A loud hovering sound ripped through the air seconds later, and each girl looked up expectantly.

"Right on time," Flora stated, eyeing the black helicopter that began its descent a few metres above them.

"There they are, get them!"

The girls looked down to see a group of six or so guards standing on the street, each one armed with a shiny, silver pistol glinting in the light.

"Go!" she shouted as a rope was flung down from above. Aqua quickly jumped a few bars up, latching onto the material and began to climb. A shot rang through the air, barely scraping the concrete to the side of the building.

Thorn instantly followed, pulling Pearl up with her as they scurried up hurriedly. Once Flora had made sure they were far enough up, she pulled herself onto the rope and gave three tugs. More shots were fired as the copter began to fly upward, avoiding the deadly bullets.

They felt the rope being lifted upwards by one of the crew on board. Aqua was already inside and helping them to get the others up, when one last shot was fired.

Striking Flora directly in the leg.

She screamed in pain as the bullet pierced her skin, immediately clutching it on instinct while keeping a tight gasp on the rope.

"Flora!" the other girls shouts of worry barely registered in her mind as she struggled use all of her willpower to hang on to the rope.

"Just hang on, you're almost there!" Pearl's cry travelled down.

All three girls frantically pulled the remaining rope ladder up as fast as they could, each worried for their friends safety. After what seemed like forever, Flora felt herself be lifted out of the bitter cold air. The crew member; a teenage boy with black hair and red eyes filled with worry, carried her to the back of the copter and placed her down gently.

"Quick, someone get me a cloth!" Thorn shouted as her medical side kicked in. "We need to apply pressure to the wound, it's not big but she could still lose a lot of blood."

Flora ripped her mask off, revealing her long brown hair a sparkling green eyes. With difficulty, she sat up and took one look at her leg and gasped. There was blood flowing heavily from the wound, and the hole where it had entered through would put her off food for days.

"Leaf! Lay back down, it's not good for you to be sitting up after that," Pearl shouted in a panicky voice.

Ignoring her friends comment, the brunette gazed once again at her leg, quickly wishing she hadn't. Aqua rushed off to find some sort of material, and moments later she returned with a black t-shirt, but they were too concerned to pay attention to what they would have normally found strange.

"Here," Aqua said, holding out the item. Thorn hurriedly took of her gloves and grabbed it, wrapping the makeshift bandage around Flora's leg to help stop the blood flowing. The girl whimpered in pain, but tried to remain strong for her group.

Pearl's cobalt eyes were filled with concern as she stood to the side. Aqua joined her moments later, watching as Thorn carefully attended to Flora's leg wound.

"Will she be okay?" a male voiced asked from behind the injured girl.

Thorn smiled at the speaker, "She'll be fine as long as we keep applying pressure to the wound."

He was about to reply, when a wind turbulence rocked the copter forcefully. Flora winced as Thorn grabbed her leg in an attempt to keep it in place.

"Just relax, we'll be back at the base soon. They can take care of you there," Thorn soothed, immediately easing the wounded leg back into a more comfortable position.

Flora managed a small smile, before finally obeying and lied back down again. It wasn't long before the girls voices became nothing but distant echoes and she lost consciousness.

* * *

**The streets of Silvertown, Johto – Normal POV**

Five men dressed in identical, expensive black suits stood back from the sixth as he fired one last shot at the copter. Whether it hit what he was aiming for none of them could be sure of, the only thing he knew was that the enemy had gotten away.

"Damn!" he swore, smashing his pistol to the ground in fury.

His men flinched, but retained their composure. They were supposed to be the best in the business after all, which was the exact reason they had been given those two targets to protect. At times like these, failure was not an option.

And they had failed.

Failure was not a feeling any of the men were accustomed with, seeing as they had never failed a mission before. Yet somehow, four mysterious beings had managed to infiltrate on of the most well protected headquarters in all of Johto.

Their leader, being the man who had smashed his gun to the ground only moments ago, felt his mobile vibrate in his pocket. Instantly, he snatched it out and answered, "What did you find out?" he barked.

"_We found no evidence or traces of a mark anywhere! It's like they were never even here at all," _the voice replied.

"Impossible," the man snarled.

"_Hold on, I've just been told they found something!" _After several seconds of muffled voices and static, the voice finally replied, _"Sir, we know who it was," _they told him slowly.

"Well spit it out then," he demanded.

The answer made him clench his fists in fury, yet a course of dread ran through his body at the three letter word.

"_The Shadow Sisters."_

* * *

**Shadow Academy, Mount Moon, Kanto – Normal POV**

A middle aged man stood at his window, idly watching the pupils continue their daily routines when the phone rang. Instantly, he whirled around to pick it up, grasping it tightly.

"Any news?" he asked, tightening his grip.

"_Sir, Lunar and Astrid have been taken out,"_ a feminine voice through the receiver spoke professionally, but he could tell that he words were laced with hurt.

The news nearly made him drop the phone, and it took all of the man's willpower to keep a calm stance. "Who was your informer?" he eventually managed to choke out.

"_Pluto, she called only minutes ago. Do you have any idea who could be behind it? This has been the eighth one in six months!" _the woman whispered.

"I am well aware of our situation, Mars, and you know well enough who is behind it. The question is, where will she make them strike next?" he continued, trying to contain a profession stature.

"_I'm sorry Sir, I was out of line. But what does she want with them after all this time?"_

"Aries was never one to forget, no doubt she is attempting revenge for what happened."

"_But that was fifteen years ago! Surely she would ha-_

"We can talk about this later. As of now, keep those who remain of Galaxy under tight protection, we can't risk any more deaths. I think it's time we send in Group Aura."

"_But that's exactly what she wants!" _she gasped.

"I know, that's why she's not going to be expecting it," the man told her confidently.

"_Very well Sir, I'll get them in your office immediately,"_ the woman answered slowly.

"Thank you, is that all?"

"Yes Sir."

"Good then, I'll be waiting," he nodded, reaching for the 'end call' button when her voice cracked through the speaker once more.

"_Lance?"_

"Yes Delia?"

"_Be careful."_

**So how did you like it? Sorry if you didn't like the whole shooting Leaf in the leg thing, but I need to make it interesting from the beginning. To anyone that is wondering, Pearl isn't the Pearl from the games. There are codenames for each person, but I can't say much without giving anything away. Please review your thoughts!**

**Just in case any of you are actually interested, I've just started up a community that has awesome stories that totally rock! The link is at the top of my profile**


End file.
